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PloS One 2013Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique...
Desulfovibrio piezophilus strain C1TLV30(T) is a piezophilic anaerobe that was isolated from wood falls in the Mediterranean deep-sea. D. piezophilus represents a unique model for studying the adaptation of sulfate-reducing bacteria to hydrostatic pressure. Here, we report the 3.6 Mbp genome sequence of this piezophilic bacterium. An analysis of the genome revealed the presence of seven genomic islands as well as gene clusters that are most likely linked to life at a high hydrostatic pressure. Comparative genomics and differential proteomics identified the transport of solutes and amino acids as well as amino acid metabolism as major cellular processes for the adaptation of this bacterium to hydrostatic pressure. In addition, the proteome profiles showed that the abundance of key enzymes that are involved in sulfate reduction was dependent on hydrostatic pressure. A comparative analysis of orthologs from the non-piezophilic marine bacterium D. salexigens and D. piezophilus identified aspartic acid, glutamic acid, lysine, asparagine, serine and tyrosine as the amino acids preferentially replaced by arginine, histidine, alanine and threonine in the piezophilic strain. This work reveals the adaptation strategies developed by a sulfate reducer to a deep-sea lifestyle.
Topics: Adaptation, Physiological; Amino Acids; Atmospheric Pressure; Desulfovibrio; Energy Metabolism; Hydrostatic Pressure; Lipids; Multigene Family; Oceans and Seas; Oxidation-Reduction; Pressure; Proteomics; Species Specificity; Sulfates
PubMed: 23383081
DOI: 10.1371/journal.pone.0055130 -
Applied and Environmental Microbiology Apr 2002To develop a better understanding of respiration by sulfate-reducing bacteria, we examined transcriptional control of respiratory genes during growth with lactate or...
To develop a better understanding of respiration by sulfate-reducing bacteria, we examined transcriptional control of respiratory genes during growth with lactate or hydrogen as an electron donor. RNA extracts of Desulfovibrio desulfuricans subsp. aestuarii were analyzed by using random arbitrarily primed PCR. RNA was reverse transcribed under low-stringency conditions with a set of random primers, and candidate cDNAs were cloned, sequenced, and characterized by BLAST analysis. Putative differentially expressed transcripts were confirmed by Northern blot analysis. Interestingly, dissimilatory bisulfite reductase was upregulated in the presence of hydrogen. To link these transcriptional changes to the physiology of sulfate-reducing bacteria, sulfide was measured during growth of several strains of Desulfovibrio on hydrogen or lactate, and this revealed that hydrogen-grown cells produced more sulfide per unit of cell mass than lactate-grown cells. Transcription of other redox proteins was characterized by Northern blotting to determine whether or not they were also transcribed to higher levels in hydrogen-grown cells. Growth on lactate produced greater transcription of [NiFe] hydrogenase. H(2)-grown cells transcribed the adenylylsulfate reductase b subunit and HmcA to higher levels. The results we describe here provide new insight into the continuing debate over how Desulfovibrio species utilize redox components to generate membrane potential and to channel electrons to sulfate, the final electron acceptor.
Topics: Bacterial Proteins; Blotting, Northern; Desulfovibrio; Gene Expression Regulation, Bacterial; Hydrogen; Lactates; Oxidation-Reduction; Polymerase Chain Reaction; RNA, Bacterial; Sulfates; Sulfides; Transcription, Genetic
PubMed: 11916715
DOI: 10.1128/AEM.68.4.1932-1937.2002 -
Environmental Microbiology Apr 2009Rs-N31, a 16S rRNA phylotype affiliated with the genus Desulfovibrio, has frequently been detected from the gut of the wood-feeding termite Reticulitermes speratus. In...
Rs-N31, a 16S rRNA phylotype affiliated with the genus Desulfovibrio, has frequently been detected from the gut of the wood-feeding termite Reticulitermes speratus. In this study, we designed a probe specifically targeting phylotype Rs-N31 and performed fluorescence in situ hybridization to identify the corresponding cells. The signals were detected exclusively inside the cells of the flagellate Trichonympha agilis, which simultaneously harbours another intracellular bacterium belonging to the candidate phylum Termite Group 1 (TG1). The detected cells were coccoid or short rods and specifically localized in the cortical layer of mainly, the anterior part of the flagellate cell. Approximately 1800 cells were contained in a single host cell, accounting for, in total, 2% of the whole prokaryotic gut microbiota. The genes dsrAB and apsA for sulfate reduction and a gene-encoding H(2)-uptake hydrogenase, both possessing a high sequence identity with those of known desulfovibrios, were obtained by polymerase chain reaction (PCR) from the host cells isolated using a micromanipulator, and their expression was verified by reverse-transcription PCR. Thus, we suggest that this endosymbiont acts as a sink for the hydrogen generated by both the flagellates and possibly TG1 symbionts. For this uncultured bacterium, we propose a novel species, 'Candidatus Desulfovibrio trichonymphae'.
Topics: Animals; Bacterial Proteins; DNA, Bacterial; DNA, Ribosomal; Desulfovibrio; Eukaryota; Gastrointestinal Tract; Genes, rRNA; In Situ Hybridization, Fluorescence; Isoptera; Molecular Sequence Data; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; Symbiosis
PubMed: 19170725
DOI: 10.1111/j.1462-2920.2008.01827.x -
Pathogens and Disease Feb 2013
Topics: Bacteriological Techniques; DNA, Bacterial; Desulfovibrio; Feces; Humans; Molecular Diagnostic Techniques; Polymerase Chain Reaction; Stomach Diseases
PubMed: 23620113
DOI: 10.1111/2049-632X.12013 -
International Journal of Systematic... Jul 1992A novel type of sulfate-reducing bacteria with unusual morphology was isolated from an oil-producing well in the Paris Basin. The cells of this bacterium, strain SEBR...
A novel type of sulfate-reducing bacteria with unusual morphology was isolated from an oil-producing well in the Paris Basin. The cells of this bacterium, strain SEBR 2582T (T = type strain), are long, thin, flexible rods, contain desulfoviridin, and are physiologically similar to members of the genus Desulfovibrio. On the basis of 16S rRNA sequence data, this strain should be included in the genus Desulfovibrio. However, strain SEBR 2582T differs from other members of this genus morphologically, physiologically, and phylogenetically. Thus, a new species, Desulfovibrio longus sp. nov., is proposed for this organism.
Topics: Base Composition; Base Sequence; DNA, Bacterial; Desulfovibrio; Microscopy, Electron; Molecular Sequence Data; Petroleum; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Homology, Nucleic Acid; Water Microbiology
PubMed: 1380287
DOI: 10.1099/00207713-42-3-398 -
International Journal of Systematic... Jan 1998A sulfate-reducing bacterium, strain Aspo-2, was isolated from granitic groundwater sampled at a depth of 600 m. This and other strains of SRB frequently occur in the...
A sulfate-reducing bacterium, strain Aspo-2, was isolated from granitic groundwater sampled at a depth of 600 m. This and other strains of SRB frequently occur in the deep granitic rock aquifers studied. On the basis of its morphological, physiological and genotypical properties, and its unique habitat, we propose strain Aspo-2 as a new species of the genus Desulfovibrio, Desulfovibrio aespoeensis (DSM 10631T).
Topics: Cell Wall; Desulfovibrio; Fresh Water; Genes, Bacterial; Microscopy, Electron, Scanning; Molecular Sequence Data; RNA, Bacterial; RNA, Ribosomal, 16S; Sulfates; Sweden
PubMed: 9542102
DOI: 10.1099/00207713-48-1-311 -
Applied and Environmental Microbiology Nov 2018Magnetosomes are complex bacterial organelles that serve as model systems for studying bacterial cell biology, biomineralization, and global iron cycling. Magnetosome...
Magnetosomes are complex bacterial organelles that serve as model systems for studying bacterial cell biology, biomineralization, and global iron cycling. Magnetosome biogenesis is primarily studied in two closely related of the genus that form cubooctahedral-shaped magnetite crystals within a lipid membrane. However, chemically and structurally distinct magnetic particles have been found in physiologically and phylogenetically diverse bacteria. Due to a lack of molecular genetic tools, the mechanistic diversity of magnetosome formation remains poorly understood. RS-1 is an anaerobic sulfate-reducing deltaproteobacterium that forms bullet-shaped magnetite crystals. A recent forward genetic screen identified 10 genes in the conserved magnetosome gene island of that are essential for its magnetic phenotype. However, this screen likely missed mutants with defects in crystal size, shape, and arrangement. Reverse genetics to target the remaining putative magnetosome genes using standard genetic methods of suicide vector integration have not been feasible due to the low transconjugation efficiency. Here, we present a reverse genetic method for targeted mutagenesis in using a replicative plasmid. To test this method, we generated a mutant resistant to 5-fluorouracil by making a markerless deletion of the gene that encodes uracil phosphoribosyltransferase. We also used this method for targeted marker exchange mutagenesis by replacing , a gene identified in our previous screen as a magnetosome formation factor, with a streptomycin resistance cassette. Overall, our results show that targeted mutagenesis using a replicative plasmid is effective in and may also be applied to other genetically recalcitrant bacteria. Magnetotactic bacteria (MTB) are a group of organisms that form intracellular nanometer-scale magnetic crystals though a complex process involving lipid and protein scaffolds. These magnetic crystals and their lipid membranes, termed magnetosomes, are model systems for studying bacterial cell biology and biomineralization and are potential platforms for biotechnological applications. Due to a lack of genetic tools and unculturable representatives, the mechanisms of magnetosome formation in phylogenetically deeply branching MTB remain unknown. These MTB contain elongated bullet-/tooth-shaped magnetite and greigite crystals that likely form in a manner distinct from that of the cubooctahedral-shaped magnetite crystals of the genetically tractable MTB within the Here, we present a method for genome editing in RS-1, a cultured representative of the deeply branching MTB of the class This marks a crucial step in developing as a model for studying diverse mechanisms of magnetic particle formation by MTB.
Topics: Anaerobiosis; Desulfovibrio; Gene Editing; Genome, Bacterial; Magnetosomes; Mutagenesis; Plasmids; Reverse Genetics
PubMed: 30194101
DOI: 10.1128/AEM.01724-18 -
Systematic and Applied Microbiology Dec 1998A mesophilic strain of sulfate-reducing bacterium, designated ALA-3T (T = type strain), was isolated from an anaerobic lagoon of a dairy wastewater treatment plant. The...
A mesophilic strain of sulfate-reducing bacterium, designated ALA-3T (T = type strain), was isolated from an anaerobic lagoon of a dairy wastewater treatment plant. The curved, Gram-negative, non-sporeforming cells (0.2 x 3.0-4.0 microns) existed singly or in chains, and were motile by single polar flagella. Optimum growth occurred at 35 degrees C and pH 7.5 on a medium containing lactate and sulfate. Thiosulfate or sulfite but not elemental sulfur, nitrate, or fumarate could also replace sulfate as an electron acceptor. Formate, alanine, aspartate, leucine, isoleucine, valine, and methionine, H2/CO2 and ethanol also served as electron donors with sulfate as an electron acceptor. Pyruvate, casamino acids, peptone, serine, glycine, cysteine and threonine were fermented. Sulfite and thiosulfate were disproportionated to sulfate and sulfide. The G + C content of the DNA was 66 mol % G + C. Phylogenetic analysis revealed that Desulfovibrio africanus was the nearest relative (similarity of 89%). Strain ALA-3T is physiologically and phylogenetically different from other Desulfovibrio species, and is designated Desulfovibrio aminophilus sp. nov. (DSM 12254).
Topics: Amino Acids; Anaerobiosis; DNA, Bacterial; Desulfovibrio; Environmental Microbiology; Hydrogen-Ion Concentration; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Sewage; Sulfates; Temperature
PubMed: 9924817
DOI: 10.1016/S0723-2020(98)80061-1 -
Journal of Biological Inorganic... Mar 2015The activity of sulfate-reducing bacteria (SRB) intensifies the problems associated to corrosion of metals and the solution entails significant economic costs. Although...
The activity of sulfate-reducing bacteria (SRB) intensifies the problems associated to corrosion of metals and the solution entails significant economic costs. Although molybdate can be used to control the negative effects of these organisms, the mechanisms triggered in the cells exposed to Mo-excess are poorly understood. In this work, the effects of molybdate ions on the growth and morphology of the SRB Desulfovibrio alaskensis G20 (DaG20) were investigated. In addition, the cellular localization, ion uptake and regulation of protein expression were studied. We found that molybdate concentrations ranging between 50 and 150 µM produce a twofold increase in the doubling time with this effect being more significant at 200 µM molybdate (five times increase in the doubling time). It was also observed that 500 µM molybdate completely inhibits the cellular growth. On the context of protein regulation, we found that several enzymes involved in energy metabolism, cellular division and metal uptake processes were particularly influenced under the conditions tested. An overall description of some of the mechanisms involved in the DaG20 adaptation to molybdate-stress conditions is discussed.
Topics: Cell Proliferation; Desulfovibrio; Ions; Metabolic Networks and Pathways; Molybdenum
PubMed: 25488518
DOI: 10.1007/s00775-014-1224-4 -
International Journal of Systematic and... Sep 2004Two moderately halophilic, mesophilic, sulfate-reducing bacteria were isolated from production-water samples from Emeraude Oilfield, Congo. Motile, vibrioid cells of...
Two moderately halophilic, mesophilic, sulfate-reducing bacteria were isolated from production-water samples from Emeraude Oilfield, Congo. Motile, vibrioid cells of SRL4225T grew optimally at a concentration of 4 % NaCl, at pH 5.8-6.2, with a minimal pH for growth of 5.2, showing that it is a moderately acidophilic bacterium. Cells of SRL6146T were motile, curved or vibrioid, long and thin rods. Optimal growth was obtained at a concentration of 5-6 % NaCl, at pH 6.8-7.2. The nutritional requirements showed that many of the characteristics of these strains overlap with those of known Desulfovibrio species. On the basis of 16S rRNA gene sequence analysis and DNA-DNA hybridization studies, both strains are members of the genus Desulfovibrio. However, they are not closely related to any species of the genus that have validly published names. It is therefore proposed that the two strains are members of two novel species of the genus Desulfovibrio with the names Desulfovibrio bastinii sp. nov. (type strain SRL4225T = DSM 16055T = ATCC BAA-903T) and Desulfovibrio gracilis sp. nov. (type strain SRL6146T = DSM 16080T = ATCC BAA-904T).
Topics: Anti-Bacterial Agents; Bacterial Typing Techniques; Congo; DNA, Bacterial; DNA, Ribosomal; Desulfovibrio; Genes, rRNA; Hydrogen-Ion Concentration; Microscopy, Phase-Contrast; Molecular Sequence Data; Movement; Nucleic Acid Hybridization; Oxidation-Reduction; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Saline Solution, Hypertonic; Sequence Analysis, DNA; Sulfates; Temperature; Water Microbiology
PubMed: 15388730
DOI: 10.1099/ijs.0.02977-0